GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpE in Pseudomonas fluorescens FW300-N2E2

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate Pf6N2E2_1717 Anthranilate synthase, aminase component (EC 4.1.3.27)

Query= curated2:O66849
         (494 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1717
          Length = 489

 Score =  263 bits (672), Expect = 1e-74
 Identities = 154/367 (41%), Positives = 221/367 (60%), Gaps = 21/367 (5%)

Query: 124 GYFAYDVVKFYEPVEDKNPDPIHTYDIYLVLTDVVVIHDNLTGKIKVVVPIFAQNGIEEE 183
           GYF+YD V+  E + D       TYD  L+   V              +  F  NGI E 
Sbjct: 132 GYFSYDCVRLIERLPDLAKQ---TYDYPLIALSVYQ-----------TLVYFHSNGIVET 177

Query: 184 YERAKNL-----IRDTVKKLKERGTTFLNVVEKEPDFKNWRSNFTKEEFEDIVKKAKEYI 238
                +L     + D         +  L  +     F+  R+  T E+F + V+ A E+I
Sbjct: 178 LINNHDLWSPRTLEDYPFLSSTPASEALAPLPYPEGFEEERT-VTPEQFVERVEVAMEHI 236

Query: 239 AQGDVIQVVLSQRFRKRFKGNPDNIYRVLRFLNPSPYMYYLDFDQLKVIGSSPEILVRLE 298
             GDV Q+ L    R R + +P ++Y+ LR  NPSPYMY      + +IG+SPE+ VR++
Sbjct: 237 RAGDVYQIQLGHEIRIRSQVSPFDVYQNLRLRNPSPYMYLAHVGGIDLIGASPELFVRIK 296

Query: 299 EGRIETRPIAGTRKRGRTEEEDKRLEEDLLSDEKERAEHLMLVDLARNDIGRVAKTGSVR 358
           +  IE RPIAGT  + +   +  +L  +L   EKERAEHLML+DL RNDIGRV + GS+ 
Sbjct: 297 DDLIEMRPIAGTVGK-KPGVDPTQLVLELTRSEKERAEHLMLIDLCRNDIGRVCQAGSLE 355

Query: 359 VENFMRIERYSHVMHIVSDVVGELREGYDALDVLKATFPAGTVSGAPKVRAMQIIEELEN 418
           V+ FM +E YSH+ H+VS+V G LR G DA DV+KA+FPAGT+SGAPKVRAM++IE +E+
Sbjct: 356 VDEFMLVEEYSHLYHMVSNVRGLLRPGLDAFDVIKASFPAGTMSGAPKVRAMELIEGMES 415

Query: 419 ERRGIYAGSVGYISFQGNMDMAIAIRTAVYRDRDIFVQAGAGIVADSVPEKEWEETVNKA 478
            RRGIYAG++G + F G+++ A+ IR+ V+ +    ++A AG+VADSVPE EW+ET+ K 
Sbjct: 416 NRRGIYAGALGLVGFDGSVNTALCIRSTVFDEGTYHLRASAGVVADSVPELEWKETLYKM 475

Query: 479 KALMKAI 485
            ++ +A+
Sbjct: 476 GSVYRAV 482


Lambda     K      H
   0.318    0.138    0.390 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 527
Number of extensions: 21
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 494
Length of database: 489
Length adjustment: 34
Effective length of query: 460
Effective length of database: 455
Effective search space:   209300
Effective search space used:   209300
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory